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Project 9201 moving to Full FAH by jadeshi » Sun Jul 13, 2014 2:49 pmNew GPU Project 9201
Postby jadeshi » Wed Apr 23, 2014 8:05 am
Project description here: http://fah-web.stanford.edu/cgi-bin/fah ... ned?p=9201 (fah-web seems to be down at the moment of this post, however)
Transcribed (roughly):
This project is a simulation of Pin1 WW domain, which is a 40-residue protein arranged in an anti-parallel, 3-stranded beta sheet in the native state. It has been studied extensively in literature as a model system for the folding of beta sheets in general. Because beta sheets are ubiquitous structures in the proteome, gaining a firm understanding of the folding dynamics of this small representative system could potentially provide insights into the folding dynamics of countless other proteins. Experiments have suggested that the rate-limiting step to folding involves formation of the loop between the first and second strands, though no higher resolution structural information of the folding mechanism is available. This simulation will aim to establish an atomistic picture of the transition state ensemble and dominant folding pathways.
The long term vision of this project is to use the information obtained through the simulation to design small molecules to catalyze folding (i.e. stabilize the transition state). This small molecule catalysis methodology has direct applications to combating common protein misfolding diseases such as Alzheimer's and Parkinson's disease, and represents an alternative to the typical approach of directly destabilizing misfolded structures.
Specs:
OS: Win/Linux
stats credit: 8000
k-factor: 0.75
timeout: 2.6
deadline: 3.4
n_atoms: 20000
min core version: 46
contact: jadeshi@stanford.edu
Thanks!
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P9102 moving to adv
Unread postby msultan » Fri May 23, 2014 7:56 am New GPU Project P9102
Unread postby msultan » Thu May 22, 2014 2:44 am
Hello all,
I am releasing 9102 to beta. It should be pretty stable since it was designed to adaptively sample the under sampled regions from the results of p9101. The points are the same as before. Let me know if some minor tweaking is required.
Project Info:
The fyn kinase is an enzyme present in multiple signaling pathways whose aberrant behavior leads to cancerous cell growth, and has also been implicated in the invasion of the dengue virus. This project continues the Pande Lab's effort to map out the conformational landscape of the src kinase family. Recent work from our lab on a similar kinase found a potentially druggable intermediate state(Shukla et al, Nature2014). The main aim of the present simulation is to get a better understanding of Fyn's dynamics in order to design better therapeutics.
More Science:
The link between fyn and dengue: http://www.ncbi.nlm.nih.gov/pubmed/23616652
Recent Src Results: http://www.nature.com/ncomms/2014/14030 ... s4397.html
Some Project Stats:
client-type beta
timeout 8.0
deadline 10.0
k-factor 0.75
gens 2000
min-core-version 46
natoms ~33000
stats-credit 4000
对于A卡来讲相比其他CORE17包PPD偏低约15-20%,
290只有15.6万PPD,平均低了3万PPD
对于N卡基本上持平
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发表于 2014-5-22 10:27:03
发表于 2014-5-23 10:47:42
发表于 2014-5-23 11:17:10